Recent Perspective of Next Generation Sequencing: Applications in Molecular Plant Biology and Crop Improvement

Yadav, Prashant; Vaidya, Era; Rani, Reema; Yadav, Navneet Kumar; Singh, Bhupender; Rai, P. K.; Singh, Dhiraj

doi:10.1007/s40011-016-0770-7

Cited by 21 publications

(14 citation statements)

References 128 publications

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“…The Next-Generation Sequencing platforms comprise rapidly evolving high throughput methods that are selected to produce new insights into the genome, transcriptome and epigenome of plants to assist the breeders in understanding the biological function of the genes [33]. Transcriptomics studies allow the identification of pathways that are regulated at the osmotic and ionic phases.…”

Section: Introductionmentioning

confidence: 99%

Transcriptome profiling at osmotic and ionic phases of salt stress response in bread wheat uncovers trait-specific candidate genes

et al. 2020

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Background Bread wheat is one of the most important crops for the human diet, but the increasing soil salinization is causing yield reductions worldwide. Improving salt stress tolerance in wheat requires the elucidation of the mechanistic basis of plant response to this abiotic stress factor. Although several studies have been performed to analyze wheat adaptation to salt stress, there are still some gaps to fully understand the molecular mechanisms from initial signal perception to the onset of responsive tolerance pathways. The main objective of this study is to exploit the dynamic salt stress transcriptome in underlying QTL regions to uncover candidate genes controlling salt stress tolerance in bread wheat. The massive analysis of 3′-ends sequencing protocol was used to analyze leave samples at osmotic and ionic phases. Afterward, stress-responsive genes overlapping QTL for salt stress-related traits in two mapping populations were identified. Results Among the over-represented salt-responsive gene categories, the early up-regulation of calcium-binding and cell wall synthesis genes found in the tolerant genotype are presumably strategies to cope with the salt-related osmotic stress. On the other hand, the down-regulation of photosynthesis-related and calcium-binding genes, and the increased oxidative stress response in the susceptible genotype are linked with the greater photosynthesis inhibition at the osmotic phase. The specific up-regulation of some ABC transporters and Na+/Ca2+ exchangers in the tolerant genotype at the ionic stage indicates their involvement in mechanisms of sodium exclusion and homeostasis. Moreover, genes related to protein synthesis and breakdown were identified at both stress phases. Based on the linkage disequilibrium blocks, salt-responsive genes within QTL intervals were identified as potential components operating in pathways leading to salt stress tolerance. Furthermore, this study conferred evidence of novel regions with transcription in bread wheat. Conclusion The dynamic transcriptome analysis allowed the comparison of osmotic and ionic phases of the salt stress response and gave insights into key molecular mechanisms involved in the salt stress adaptation of contrasting bread wheat genotypes. The leveraging of the highly contiguous chromosome-level reference genome sequence assembly facilitated the QTL dissection by targeting novel candidate genes for salt tolerance.

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Section: Introductionmentioning

confidence: 99%

Transcriptome profiling at osmotic and ionic phases of salt stress response in bread wheat uncovers trait-specific candidate genes

et al. 2020

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“…Recently, next generation sequencing (NGS) technologies have accelerated the screening of germplasm collections, identifying thousands of SNP markers in a cost effective and timely way [27,28]. Notably, genotyping-by-sequencing (GBS), a highly multiplexed method based on the reduction of genome complexity through methylation-sensitive restriction enzymes [29], has become a popular approach for detecting genome-wide variation in plants [30].…”

Section: Introductionmentioning

confidence: 99%

Optimization of the genotyping‐by‐sequencing SNP calling for diversity analysis in cape gooseberry (Physalis peruviana L.) and related taxa

et al. 2020

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A robust Genotyping-By-Sequencing (GBS) pipeline platform was examined to provide accurate discovery of Single Nucleotide Polymorphisms (SNPs) in a cape gooseberry (Physalis peruviana L.) and related taxa germplasm collection. A total of 176 accessions representing, wild, weedy, and commercial cultivars as well as related taxa from the Colombian germplasm bank and other world repositories were screened using GBS. The pipeline parameters mnLCov of 0.5 and a mnScov of 0.7, tomato and potato genomes, and cape gooseberry transcriptome for read alignments, were selected to better assess diversity and population structure in cape gooseberry and related taxa. A total of 7,425 SNPs, derived from P. peruviana common tags (unique 64 bp sequences shared between selected species), were used. Within P. peruviana, five subpopulations with a high genetic diversity and allele fixation (H E : 0.35 to 0.36 and F IS :-0.11 to-0.01, respectively) were detected. Conversely, low genetic differentiation (F ST : 0.01 to 0.05) was also observed, indicating a high gene flow among subpopulations. These results contribute to the establishment of adequate conservation and breeding strategies for Cape gooseberry and closely related Physalis species.

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“…The popularity of sequencing technology has driven an unprecedented development of omics [7]. Attempts by breeders and scientists to expound on the genetic mechanism of heterosis at the molecular level show promise [8,9].…”

Section: Introductionmentioning

confidence: 99%

Transcriptome and Metabolite Profiling Reveal Novel Insights into Volatile Heterosis in the Tea Plant (Camellia Sinensis)

et al. 2019

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Tea aroma is a key indicator for evaluating tea quality. Although notable success in tea aroma improvement has been achieved with heterosis breeding technology, the molecular basis underlying heterosis remains largely unexplored. Thus, the present report studies the tea plant volatile heterosis using a high-throughput next-generation RNA-seq strategy and gas chromatography–mass spectrometry. Phenotypically, we found higher terpenoid volatile and green leaf volatile contents by gas chromatography–mass spectrometry in the F1 hybrids than in their parental lines. Volatile heterosis was obvious in both F1 hybrids. At the molecular level, the comparative transcriptomics analysis revealed that approximately 41% (9027 of 21,995) of the genes showed non-additive expression, whereas only 7.83% (1723 of 21,995) showed additive expression. Among the non-additive genes, 42.1% showed high parental dominance and 17.6% showed over-dominance. Among different expression genes with high parental dominance and over-dominance expression patterns, KEGG and GO analyses found that plant hormone signal transduction, tea plant physiological process related pathways and most pathways associated with tea tree volatiles were enriched. In addition, we identified multiple genes (CsDXS, CsAATC2, CsSPLA2, etc.) and transcription factors (CsMYB1, CsbHLH79, CsWRKY40, etc.) that played important roles in tea volatile heterosis. Based on transcriptome and metabolite profiling, we conclude that non-additive action plays a major role in tea volatile heterosis. Genes and transcription factors involved in tea volatiles showing over-dominance expression patterns can be considered candidate genes and provide novel clues for breeding high-volatile tea varieties.

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Recent Perspective of Next Generation Sequencing: Applications in Molecular Plant Biology and Crop Improvement

Cited by 21 publications

References 128 publications

Transcriptome profiling at osmotic and ionic phases of salt stress response in bread wheat uncovers trait-specific candidate genes

Transcriptome profiling at osmotic and ionic phases of salt stress response in bread wheat uncovers trait-specific candidate genes

Optimization of the genotyping‐by‐sequencing SNP calling for diversity analysis in cape gooseberry (Physalis peruviana L.) and related taxa

Transcriptome and Metabolite Profiling Reveal Novel Insights into Volatile Heterosis in the Tea Plant (Camellia Sinensis)

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